It seems like once you get out of the top shonen animes like One Piece, Fairy Tail, Gintama, Naruto, and Bleach that there is a over whelming trend towards male main characters being weak willed and whimpy usually accompanied by a strong female character. why is this? Is it really that popular in Japan to have male main characters like that?

I think there's a certain slice where this is the case, but definitely not all around. Most 'serious' anime have incredibly powerful male leads that are very unyielding. Even Eyeshiled 21 - thoroughly humorous - had a number of very egotistical/powerful male leads. Fate/Zero had Kotomine, Rider and Gilgamesh, in fact nearly every male character in that show was powerful...I think I could keep at this if I keep thinking back through what I've watched...what sort of shows did you have in mind?

I think that it may be the fact of starting the main character weak willed and faced with overwhelming opponents. This allows for you to watch over the mass of episodes showing how the character becomes stronger and stronger through the varying situations. The strong female supporting character is set in place to give the main character a reason to fight with such intention to protect what he loves (Also for fan service opportunities). For instance, in Bleach

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Ichigo goes super hollow after hearing Orihime cry and he comes back from the dead.

Character development opportunities, and so the audience can "relate" to a "realistic" person. Although if you end up with a protagonist too much like Shinji Ikari it can backfire on you (he was a carefully crafted character, not a template).

But if you start right off with a full-powered Superman there's not much you can do besides just tell the audience more and more about him, since it's hard to change him or build him up any higher at all. If you have sufficiently complex characters this is fine (see: Cowboy Bebop), but it's definitely easier to start off with a weakling who has problems that you can fix as you go along - it gives you tons of material you can use for building character arcs throughout the series.

I agree that I wish anime had more confident protagonists, though.

It's possible to relate to a character through aspiration as well as "he sucks just as much as a depressed otaku who can't take personal responsibility for himself and needs a strong-willed woman in his life to motivate him."

Or something like that.

It could also have deep societal roots. The "lone hero/badass" character is much further outside the social structure of Japan than the United States, unless you go back to the Sengoku period. And they're under a lot of social pressure.

If I was in Japan watching the news every night, I'm not sure I'd be dreaming up confident protagonists either.

I think it really depends on the show. to be honest I would rather have a main character who isn't super OP. I find that most of the longer running beat em up type shows get boring because its always the same thing of the OP character kicking butt without there ever being anything new. I mean even in bleach I got tired of watching Ichigo lose the first fight with an opponent (so the bad guy could be introduced) only to come back and dominate the fight the second time around.

I think it really depends on the show. to be honest I would rather have a main character who isn't super OP. I find that most of the longer running beat em up type shows get boring because its always the same thing of the OP character kicking butt without there ever being anything new. I mean even in bleach I got tired of watching Ichigo lose the first fight with an opponent (so the bad guy could be introduced) only to come back and dominate the fight the second time around.

He doesn't have to be powerful from the beginning for instant the main character from Attack on Titan isn't whimpy or weak willed he's just inexperienced which leaves him room to grow.

thats why I prefer shows that have a weaker starting character over an over powered one. It leaves room for growth and provides a struggle to do so. It also adds a bit more excitement when they do succeed because of what they overcame to do so

The male main protagonist, Shinya Kougami, from Psycho Pass is an example of that "strong and masculine" type of main character.

It's all about growth with (most) characters. If every main character was an overpowered god of the universe then it would get boring really fast. Having a main character with flaws puts in a slot for character development (not to say strong masculine types can't have character development as well, it's just harder to achieve). Of course, others have said this in the posts above (and probably a lot better than I).

Personally, I think every show at least needs some type of Shinji Ikari in their story.

The male main protagonist, Shinya Kougami, from Psycho Pass is an example of that "strong and masculine" type of main character.

It's interesting when characters like this are portrayed as flawed for what we in the "West" consider to be strengths. Although in Kougami's case it's more reflective of something being wrong with the social structure he's born within.

Although that itself could be a reference to modern Japanese culture - I don't know enough about it to tell.

The male main protagonist, Shinya Kougami, from Psycho Pass is an example of that "strong and masculine" type of main character.

It's interesting when characters like this are portrayed as flawed for what we'd consider to be strengths. Although in Kougami's case it's more reflective of something being wrong with the social structure he's born within.

Gurren Lagann would be a near-perfect fit for this question as well. You start out with two male protagonists (one weak and one strong), and a strong female character (with a supportive female character coming in awhile later).

it's an attempt to defy male/female presumed gender roles making it enjoyable for all audiences

I don't think that's it especially since a lot of the times the weak male character paired with strong female animes tend to also be harems which is just pandering to male fantasies not knocking down gender roles.

It's possible to relate to a character through aspiration as well as "he sucks just as much as a depressed otaku who can't take personal responsibility for himself and needs a strong-willed woman in his life to motivate him."